Proposed root cause and fix in https://chromium-review.googlesource.com/c/chromium/src/+/989431 :

The heuristic wasn't working right due to using the wrong frame as
timing reference, resulting in overthrottling for fast applications
and excessive latency for slow applications.

When estimating the render time for a frame that was already complete at
the time of check, it uses the time-until-copied as a lower bound, but
accidentally used the copy time of the currently processing frame as
opposed to the copy time of the previous rendering frame, resulting in
overestimating the render time.

Also, the heuristic to decide when to skip VSync also should have used
the currently rendering frame (two frames back when sending a new
animating frame), but was erroneously using the currently processing
frame (one frame back). Fix this, and adjust the heuristic to more
accurately reflect the intended scheduling.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/41f4ef7c623c7ae636f8666a844a12d42068ad2f

commit 41f4ef7c623c7ae636f8666a844a12d42068ad2f
Author: Klaus Weidner <klausw@chromium.org>
Date: Sun Apr 01 11:27:19 2018

Fix WebVR VSync scheduling heuristic

The heuristic wasn't working right due to using the wrong frame as
timing reference, resulting in overthrottling for fast applications
and excessive latency for slow applications.

When estimating the render time for a frame that was already complete at
the time of check, it uses the time-until-copied as a lower bound, but
accidentally used the copy time of the currently processing frame as
opposed to the copy time of the previous rendering frame, resulting in
overestimating the render time.

Also, the heuristic to decide when to skip VSync also should have used
the currently rendering frame (two frames back when sending a new
animating frame), but was erroneously using the currently processing
frame (one frame back). Fix this, and adjust the heuristic to more
accurately reflect the intended scheduling.

Bug:  827811 
Change-Id: Ic4884ccaee6f2f6d3051ce2790132582dba6702a
Reviewed-on: https://chromium-review.googlesource.com/989431
Commit-Queue: Ian Vollick <vollick@chromium.org>
Reviewed-by: Ian Vollick <vollick@chromium.org>
Cr-Commit-Position: refs/heads/master@{#547398}
[modify] https://crrev.com/41f4ef7c623c7ae636f8666a844a12d42068ad2f/chrome/browser/android/vr/vr_shell_gl.cc

The CL from comment #2 seems to be effective according to the automated performance tests, the pose prediction time estimate looks improved:

https://chromeperf.appspot.com/report?sid=da922c1ae79febbe864da71ddef7c89cb93a6ccf5845d14bb59ceb8800161a3a&start_rev=542416&end_rev=547479